Genomic architecture of phenotypic extremes in a wild cervid

Abstract

Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

Epigenetics and island-mainland divergence in an insectivorous small mammal

“…Here, insular masked shrews exhibited different phenotypes than their mainland counterparts; morphologically, this presented as decreased body length, mass, and skull length on islands. Body size is a polygenic trait (Posbergh & Huson, 2021) with many underlying mechanisms, often making it difficult to clearly understand the role of each gene or pathway involved (e.g., Anderson et al, 2022). DNA methylation has been suggested as a universal mechanism that regulates body mass and morphological development in animals (Cao et al, 2015; Haghani et al, 2021), and appears to help regulate intra-species differences in island-mainland settings.…”

“…Here, insular masked shrews exhibited different phenotypes than their mainland counterparts; morphologically, this presented as decreased body length, mass, and skull length on islands. Body size is a heritable polygenic trait in mammals (Posbergh & Huson, 2021;Postma, 2014) with many underlying mechanisms, often making it difficult to clearly understand the role of each gene or pathway involved (e.g., Anderson et al, 2022). Cytosine methylation levels measured in highly conserved stretches of DNA have been linked to mammalian traits such as maximum lifespan (Haghani et al, 2021) and has been suggested as a universal mechanism to regulates body mass and morphological development in animals in other association studies (Cao et al, 2015;Haghani et al, 2021).…”

Genomic correlates for migratory direction in a free-ranging cervid

“…Mule deer and white-tailed deer can hybridize (Stubblefield, Warren, & Murphy, 1986), so we opted to use the long-read-based draft genome of white-tailed deer ( Odocoileus virginianus ) (Accession No. JAAVWD000000000) that was recently annotated (Anderson, Côté, Richard, & Shafer, 2022); we note that the available mule deer genome is simply a consensus sequence from reads mapped to earlier versions of the white-tailed reference (Russell et al, 2019). We performed initial quality filtering for all reads using fastqc and trimmed reads for quality and adaptors using the default Trimmomatic v.0.36 settings (Bolger et al 2014).…”

“…We used the program Gowinda v1.12 (Kofler & Schlötterer, 2012) to determine GO term enrichment while accounting for gene length biases. We created a .gtf version of our annotation by removing duplicated genes, retaining only the longest version of each gene, which resulted in 15,395 unique genes in the annotation (Anderson et al, 2022). All outlier SNPs that SnpEff identified as being on or within 25kbp of genic regions were used to analyze gene ontology and compared to all outlier SNPs in every qualifying window.…”

Genomic correlates for migratory direction in a free-ranging cervid

“…We used the program Gowinda v. 1.12 [65] to determine GO term enrichment while accounting for gene length biases. We created a .gtf version of our annotation by removing duplicated genes, retaining only the longest version of each gene, which resulted in 15 395 unique genes in the annotation [49]. All outlier SNPs that SnpEff identified as being on or within 25 kbp of genic regions were used to analyze gene ontology and compared to all outlier SNPs in every qualifying window.…”